6GCS

Cryo-EM structure of respiratory complex I from Yarrowia lipolytica


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structure of respiratory complex I at work.

Parey, K.Brandt, U.Xie, H.Mills, D.J.Siegmund, K.Vonck, J.Kuehlbrandt, W.Zickermann, V.

(2018) Elife 7

  • DOI: 10.7554/eLife.39213
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Mitochondrial complex I has a key role in cellular energy metabolism, generating a major portion of the proton motive force that drives aerobic ATP synthesis. The hydrophilic arm of the L-shaped ~1 MDa membrane protein complex transfers electrons fro ...

    Mitochondrial complex I has a key role in cellular energy metabolism, generating a major portion of the proton motive force that drives aerobic ATP synthesis. The hydrophilic arm of the L-shaped ~1 MDa membrane protein complex transfers electrons from NADH to ubiquinone, providing the energy to drive proton pumping at distant sites in the membrane arm. The critical steps of energy conversion are associated with the redox chemistry of ubiquinone. We report the cryo-EM structure of complete mitochondrial complex I from the aerobic yeast Yarrowia lipolytica both in the deactive form and after capturing the enzyme during steady-state activity. The site of ubiquinone binding observed during turnover supports a two-state stabilization change mechanism for complex I.


    Organizational Affiliation

    Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University Frankfurt, Frankfurt, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
75-KDA PROTEIN (NUAM)A728Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuamB0I71DRAFT_14167YALI1_D07089g
EC: 1.6.99.3
Find proteins for Q9UUU3 (Yarrowia lipolytica)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
51-KDA PROTEIN (NUBM)B488Yarrowia lipolyticaMutation(s): 0 
Gene Names: nubmNUO51YALI1_B26679g
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Mitochondrial Complex I in deactive form
Find proteins for Q9UUU2 (Yarrowia lipolytica)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
49-KDA PROTEIN (NUCM)C466Yarrowia lipolyticaMutation(s): 0 
Gene Names: nucmB0I71DRAFT_131656YALI1_F22993g
EC: 1.6.99.3
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
NIMM SUBUNITD87Yarrowia lipolyticaMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Mitochondrial Complex I in deactive form
Find proteins for B5FVD3 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
NUEM SUBUNITE375Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
NUFM SUBUNITF144Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30-KDA PROTEIN (NUGM)G281Yarrowia lipolyticaMutation(s): 0 
Gene Names: nugmB0I71DRAFT_126141
EC: 1.6.99.3
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
24-KDA SUBUNIT (NUHM)H243Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuhmB0I71DRAFT_136742
EC: 1.6.99.3
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
TYKY SUBUNIT (NUIM)I229Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuimB0I71DRAFT_132693YALI1_F01456g
EC: 1.6.99.3
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
NUJM SUBUNITJ198Yarrowia lipolyticaMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Mitochondrial Complex I in deactive form
Find proteins for Q6C674 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
PSST SUBUNIT (NUKM)K210Yarrowia lipolyticaMutation(s): 0 
Gene Names: nukmB0I71DRAFT_136033YALI1_F09003g
EC: 1.6.99.3
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
ND4L SUBUNIT (NULM)L86Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Mitochondrial Complex I in deactive form
Find proteins for Q9B6D4 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
NUMM SUBUNITM136Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
ACPM1 SUBUNITO109Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
NB4M SUBUNITP124Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
ACPM2 SUBUNITQ132Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
NI2M SUBUNITR109Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
NESM SUBUNITS159Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
NUPM SUBUNITU172Yarrowia lipolyticaMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Mitochondrial Complex I in deactive form
Find proteins for Q6CGB4 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
NB6M SUBUNITW123Yarrowia lipolyticaMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Mitochondrial Complex I in deactive form
Find proteins for B5FVF8 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
NUXM SUBUNITX169Yarrowia lipolyticaMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Mitochondrial Complex I in deactive form
Find proteins for Q6C4A6 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
NUYM SUBUNITY161Yarrowia lipolyticaMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Mitochondrial Complex I in deactive form
Find proteins for Q6CEK9 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
NUZM SUBUNITZ137Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
NIAM SUBUNITa100Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
NEBM SUBUNITb64Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
NB2M SUBUNITc60Yarrowia lipolyticaMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Mitochondrial Complex I in deactive form
Find proteins for B5FVE5 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
NIDM SUBUNITd92Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
NUUM SUBUNITe45Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
NI8M SUBUNITf87Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
NI9M SUBUNITg63Yarrowia lipolyticaMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Mitochondrial Complex I in deactive form
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
N7BM SUBUNITh138Yarrowia lipolyticaMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Mitochondrial Complex I in deactive form
Find proteins for Q6CG53 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
UNKNOWN SUBUNITi53Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
NB5M SUBUNITj93Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuvmB0I71DRAFT_136036YALI1_F09017g
EC: 1.6.99.3
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Mitochondrial Complex I in deactive form
Find proteins for Q6ZY24 (Yarrowia lipolytica)
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
NUNM SUBUNITn93Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
ND1 SUBUNIT (NU1M)1341Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Mitochondrial Complex I in deactive form
Find proteins for Q9B6E8 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
ND2 SUBUNIT (NU2M)2469Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Mitochondrial Complex I in deactive form
Find proteins for Q9B6C8 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
ND3 SUBUNIT (NU3M)3128Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Mitochondrial Complex I in deactive form
Find proteins for Q9B6C7 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
ND4 SUBUNIT (NU4M)4486Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Mitochondrial Complex I in deactive form
Find proteins for Q9B6D6 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
ND5 SUBUNIT (NU5M)5655Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Mitochondrial Complex I in deactive form
Find proteins for Q9B6D3 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
ND6 SUBUNIT (NU6M)6185Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Mitochondrial Complex I in deactive form
Find proteins for Q9B6E9 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
NB8M SUBUNIT899Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
NIPM SUBUNIT989Yarrowia lipolyticaMutation(s): 0 
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Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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g
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
3PE
Query on 3PE

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1, 4, g
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
NDP
Query on NDP

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E
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
ZMP
Query on ZMP

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O
S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
C25 H49 N2 O8 P S
HDTINWYIVVMRIN-HSZRJFAPSA-N
 Ligand Interaction
FMN
Query on FMN

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B
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SF4
Query on SF4

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A, B, I, K
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

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A, H
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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M
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-04-19 
  • Released Date: 2018-10-10 
  • Deposition Author(s): Parey, K., Vonck, J.

Funding OrganizationLocationGrant Number
German Research FoundationGermanyEXC 115

Revision History 

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection, Structure summary
  • Version 1.2: 2019-12-11
    Changes: Other